2B4R | pdb_00002b4r

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 Angstrom Resolution reveals intriguing extra electron density in the active site

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth O]	d2b4ro1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
A [auth O]	d2b4ro2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
A [auth O]	d2b4ro4	Artifacts	Tags	Tags	Tags	C-terminal Tags	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
A [auth O]	d2b4ro3	Artifacts	Tags	Tags	Tags	N-terminal Tags	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
B [auth P]	d2b4rp1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
B [auth P]	d2b4rp2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
B [auth P]	d2b4rp4	Artifacts	Tags	Tags	Tags	C-terminal Tags	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
B [auth P]	d2b4rp3	Artifacts	Tags	Tags	Tags	N-terminal Tags	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
D [auth R]	d2b4rr1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
D [auth R]	d2b4rr2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
D [auth R]	d2b4rr4	Artifacts	Tags	Tags	Tags	C-terminal Tags	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
D [auth R]	d2b4rr3	Artifacts	Tags	Tags	Tags	N-terminal Tags	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
C [auth Q]	d2b4rq1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
C [auth Q]	d2b4rq2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
C [auth Q]	d2b4rq4	Artifacts	Tags	Tags	Tags	C-terminal Tags	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)
C [auth Q]	d2b4rq3	Artifacts	Tags	Tags	Tags	N-terminal Tags	malaria parasite P. falciparum (Plasmodium falciparum ) [TaxId: 5833 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth O]	SCOP2 Family	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like	8056133	4000077	SCOP2 (2022-06-29)
A [auth O]	SCOP2 Superfamily	GAPDH-like	8056134	3000043	SCOP2 (2022-06-29)
B [auth P]	SCOP2B Superfamily	GAPDH-like	8056134	3000043	SCOP2B (2022-06-29)
D [auth R]	SCOP2B Superfamily	GAPDH-like	8056134	3000043	SCOP2B (2022-06-29)
C [auth Q]	SCOP2B Superfamily	GAPDH-like	8056134	3000043	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth O]	YceM-like_C	e2b4rO1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.1)
A [auth O]	NAD_binding_3	e2b4rO2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (v294.1)
B [auth P]	YceM-like_C	e2b4rP1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.1)
B [auth P]	NAD_binding_3	e2b4rP2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (v294.1)
D [auth R]	YceM-like_C	e2b4rR1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.1)
D [auth R]	NAD_binding_3	e2b4rR2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (v294.1)
C [auth Q]	YceM-like_C	e2b4rQ1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.1)
C [auth Q]	NAD_binding_3	e2b4rQ2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth O]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A [auth O]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
B [auth P]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B [auth P]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
D [auth R]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D [auth R]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
C [auth Q]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C [auth Q]	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth O], B [auth P], C [auth Q], D [auth R]	glyceraldehyde-3-phosphate dehydrogenase	binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity oxidoreductase activity glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity oxidoreductase activity glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor NAD binding	ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration catabolic process ATP metabolic process energy derivation by oxidation of organic compounds purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process cellular process purine ribonucleoside diphosphate catabolic process monosaccharide metabolic process hexose metabolic process glucose metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth O], B [auth P], C [auth Q], D [auth R]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A [auth O], B [auth P], C [auth Q], D [auth R]	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family	Family
A [auth O], B [auth P], C [auth Q], D [auth R]	IPR020829	Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain	Domain
A [auth O], B [auth P], C [auth Q], D [auth R]	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain	Domain
A [auth O], B [auth P], C [auth Q], D [auth R]	IPR020830	Glyceraldehyde 3-phosphate dehydrogenase, active site	Active Site
A [auth O], B [auth P], C [auth Q], D [auth R]	IPR006424	Glyceraldehyde-3-phosphate dehydrogenase, type I	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.